from IPython.display import display
import re
from cameo import load_model
from cameo.strain_design import pathway_prediction
model = load_model("iMM904")
predictor = pathway_prediction.PathwayPredictor(model=model, compartment_regexp=re.compile(".*_c$"))
pathways = predictor.run(product="vanillin", max_predictions=5)
id | equation | lower_bound | upper_bound | |
---|---|---|---|---|
0 | MNXR5336 | NAD(+) + H2O + vanillin <=> vanillate + NADH(2... | -1000 | 1000 |
1 | MNXR5340 | formaldehyde + NAD(+) + 3,4-dihydroxybenzoate ... | -1000 | 1000 |
2 | MNXR68718 | H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... | -1000 | 1000 |
id | equation | lower_bound | upper_bound | |
---|---|---|---|---|
0 | MNXR230 | NADP(+) + H2O + 3,4-dihydroxybenzoate <=> O2 +... | -1000 | 1000 |
1 | MNXR5336 | NAD(+) + H2O + vanillin <=> vanillate + NADH(2... | -1000 | 1000 |
2 | MNXR5340 | formaldehyde + NAD(+) + 3,4-dihydroxybenzoate ... | -1000 | 1000 |
id | equation | lower_bound | upper_bound | |
---|---|---|---|---|
0 | MNXR5336 | NAD(+) + H2O + vanillin <=> vanillate + NADH(2... | -1000 | 1000 |
1 | MNXR5340 | formaldehyde + NAD(+) + 3,4-dihydroxybenzoate ... | -1000 | 1000 |
2 | MNXR14769 | NAD(+) + 3,4-dihydroxybenzoate + H2O <=> O2 + ... | -1000 | 1000 |
id | equation | lower_bound | upper_bound | |
---|---|---|---|---|
0 | MNXR5336 | NAD(+) + H2O + vanillin <=> vanillate + NADH(2... | -1000 | 1000 |
1 | MNXR5340 | formaldehyde + NAD(+) + 3,4-dihydroxybenzoate ... | -1000 | 1000 |
2 | MNXR5836 | O2 + 3.0 H(+) + NADPH + anthranilate <=> catec... | -1000 | 1000 |
3 | MNXR7067 | 3,4-dihydroxybenzoate + H(+) <=> catechol + CO(2) | -1000 | 1000 |
id | equation | lower_bound | upper_bound | |
---|---|---|---|---|
0 | MNXR5336 | NAD(+) + H2O + vanillin <=> vanillate + NADH(2... | -1000 | 1000 |
1 | MNXR5340 | formaldehyde + NAD(+) + 3,4-dihydroxybenzoate ... | -1000 | 1000 |
2 | MNXR6101 | O2 + 3.0 H(+) + NADH(2-) + anthranilate <=> ca... | -1000 | 1000 |
3 | MNXR7067 | 3,4-dihydroxybenzoate + H(+) <=> catechol + CO(2) | -1000 | 1000 |
from cameo import phenotypic_phase_plane
from cameo.util import TimeMachine
from cameo.visualization.plotting import Grid
with Grid(nrows=3) as grid:
for i, pathway in enumerate(pathways):
with TimeMachine() as tm:
pathway.plug_model(model, tm=tm)
ppp = phenotypic_phase_plane(model, variables=[model.reactions.biomass_SC5_notrace], objective=pathway.product)
ppp.plot(grid=grid, width=450, height=350, title="Pathway %i" % (i+1), axis_font_size="12pt")